Nose/ throat swab (viral)

Transcription

1 If an urgent or unusual test is required please contact the department on during routine laboratory opening hours ( Monday to Friday, Saturday) or the on-call Biomedical Scientist via switchboard at all other times or on-call microbiology consultant out of hours if urgent advice is required. This includes samples such as CSFs and others from other sterile sites. Turnaround times are provided for guidance but earlier results may be possible for urgent requests. Quality of result depends on quality of sample collection and timely transport to the lab. Please refer to our Collection of Microbiological Specimens Policy on website (under General Information) for the appropriate method of collection,specimen container and volume, and requirements for transport and storage Quantitative results will be reported with normal ranges and/ or interpretive comments. Correct interpretation of test results depends on accurate clinical details including date of onset, travel history, antibiotic therapy where relevant. Requests may be refused or pathogens missed if these are omitted. Samples will be retained for 7 days to allow additional information to be supplied by the requestor. Note that serology refers to tests that detect the antibody response to an infection, whereas molecular tests detect the genetic material of a specific pathogen, by nucleic acid amplification methods such as polymerase chain reaction (PCR). Notifiable diseases are marked in table with an asterisk (*). PHE should be notified if infection is confirmed or strongly suspected clinically to enable public health actions. South West Health Protection Unit is available in and out of hours on Footnotes: 1 Turn around times for specimens received during normal working hours. For specimens received on weekends or bank holidays additional days might need to be added. 2 If an additional test is subsequently required on a specimen, this will be performed where possible if sufficient volume is available. Samples may degrade over time, contact the laboratory for serology requests beyond the time limits in the tables Adenovirus PCR Adenovirus Amoebic serology Anti Strep antibodies EDTA blood Nose/ throat swab (viral) Eye swab Clotted blood serum gel Included in full respiratory PCR panel Combined Adenovirus/ rotavirus EIA IFAT ASO, ASOT, Anti DNase B Suspected adenovirus infection. Monitoring of blood PCR may be indicated post bone marrow transplant. Investigation of diarrhoea in children Suspected amoebic liver abscess or amoebic dysentery. Useful for investigation of possible post- Streptococcal conditions Positive results in neonates must be confirmed by ref lab, which may lengthen turnaround time in this age group. Serology positive in 95% of ALA, but can be negative in colitis. Consider faeces for microscopy (ideally fresh and warm) 7 days 3 working days 7 days Hospital for Tropical Diseases, London 5 working days 14 working days 7 working days Antibiotic assay (includes antifungals) Antibiotic levels, TDM (therapeutic drug monitoring), Gentamicin, vancomycin, tobramycin, amikacin levels etc Blood taken from lines used to administer antibiotics may give erroneous results Please give dose regimen and time of last dose Refer to BNF or trust policies for interpretation and for when Gentamicin or Vancomycin levels should be taken. For all other assays please contact a Microbiology consultant on Gentamicin & vancomycin tested 1 working day in DCH blood sciences. Others: Southmead Antibiotic Reference laboratory 1 working day (RL: one day ) Page: 1 of 15

2 Arbovirus +/- EDTA blood Dengue fever, west Nile Virus, Haemorrhagic fever. Exotic viruses. Arthropod borne viruses. Mosquito-borne viruses. Tick borne infections. Requestor should discuss with microbiology consultant as cases are likely to need discussion with Rare and Imported PHE Imported Fever Service. Pathogens It is essential to state countries visited, duration of stay and return date with full clinical details and PHE, Porton Down vaccines given 3-7 working days. (RL: 3-5 Aspergillus pptns. Precipitating serum antibodies Investigation of ABPA. May be used to investigate Farmer s lung (EAA). 10 working days Aspergillus antigen Bronchial washings Galactomannan May be useful in investigation of suspected invasive aspergillosis 10 working days 1 month Avian pptns. Poultry, budgie, parrot only Diagnosis of hypersensitivity pneumonitis. (Extrinsic allergic allveolitis) Please specify type of bird Bristol 10 working days Blood culture Blood Investigation of sepsis and deep seated infections such as infective endocarditis. Send PRIOR to commencing antibiotic therapy wherever possible. Use blood culture kits to avoid contamination. Using the same needle that has been used to take other blood s may result in false positive results. See trust blood culture policy. Sensitivity is improved by collecting adequate volume (5-10ml per bottle) and sending >1 set. Send 3 sets if IE is suspected. All positive results are telephoned 2 working days for negatives. Up to 7 working days for positives. Bordetella pertussis* serology. Whooping cough, Pertussis Diagnosis of pertussis infection after >2/52 of symptoms Investigation of suspected whooping cough or persistent cough. False negatives may occur if blood taken within 2 weeks of start of symptoms For children aged 5-16y with cough >2 weeks, who have not had pertussis vaccine in the past year, Oral fluid testing kits are the preferred test - available from PHE (on notification) Bacteriology Reference Department 21 working days (RL: 10 days) Bordetella pertussis culture* Pernasal swab. Whooping cough, Pertussis Diagnosis of pertussis infection during first 2/52 of symptoms Sensitivity can be low. Most likely to be culture positive within 2 weeks of onset. If aged under 1 and hospitalised, PCR is available. Up to 7 working days Bordetella PCR* Nasal secretion Nasopharyngeal aspirate Nasal Swab. Whooping cough, Pertussis Available for suspected whooping cough cases in inpatients under 1 year of age Bacteriology Reference Department RL: 10 working days Page: 2 of 15

3 BK virus PCR Brucella* serology Campylobacter antibodies EDTA blood Urine.. Undulant fever. B.abortus (cattle) B.melitensis (goats, sheep) For screening post renal transplant, investigation of BK virus nephropathy or haemorrhagic cystitis in the immunocompromised. Suspected Brucellosis, PUO Significant cause of Guillain Barre Refer to renal guidelines for interpretation of result. No longer endemic in UK. Give dates of travel, animal contact or unpasteurised food exposure. Royal Liverpool & Broadgreen Hosp. Liverpool FWE Microbiology Network, Preston Lancs 7 working days 7 days 10 working days 10 working days CAPD Fluid Fluid peritoneal dialysis fluid PD peritonitis An additional sample in blood culture bottles improves likelihood of positive culture. WBC >100X10^6/L suggests infection Microscopy within 2 hours if urgent (unless after 10pm). Culture 7 working days. 7 days CD4 Count EDTA blood Bournemouth Microbiology 5 working days Chlamydia Urine or yellow chlamydia swab C.trachomatis. Chlamydia NAAT (Nucleic acid amplification technique) Part of STI screen Neonatal conjunctivitis Please follow kit instructions. For women, send vaginal+/- cervical swabs. Vaginal swab can be selfcollected. For men, preferred specimen is urine after a 1 hour hold, plus rectal and throat swabs where relevant. GUM clinic samples are tested by combined chlamydia and gonorrhoea NAAT. 5 working days Chlamydia Serology Chlamydia L2 Serology is rarely helpful in genital infection except in PID or infertility 10 working days Clostridium difficile toxin Investigation of diarrhoea, particularly in the elderly and inpatients Test is performed automatically on all liquid stools from inpatients (over old) and community patients over 65 years. Occasionally equivocal result will be obtained. For inpatients, PCR will be performed on equivocal results to determine whether toxigenic C difficile bacteria are present. 1 working day 7 days CMV IgG CMV IgM CMV PCR CMV salivary PCR Corneal scrape Cytomegalovirus To determine past infection 1 working day 12 months Cytomegalovirus Test if acute infection is suspected 1 working day 2 months Useful to confirm disease process or EDTA blood Cytomegalovirus monitor treatment in Results are quantitative viral loads Urine immunosuppressed patients Bristol 3 working days 7 days Saliva swab. Contact lab under Ext 4349 to request swab Corneal scrapings Congenital CMV For investigation of congenital CMV in neonates Investigation of microbial keratitis/ corneal ulcer Contact lenses and cases should be sent to lab in addition, where available. Southampton PHE laboratory 3 working days 3 working days Page: 3 of 15

4 Coxiella burnetii serology Q fever, Queensland fever Can cause subacute bacterial endocarditis, respiratory disease, or chronic Q fever May be negative acutely, send convalescent sera too. Bristol 7 working days CRE screen Cross infection screen Rectal swab or any other wound or lesion site. Nose and groin swabs plus any wound or lesion sites Carbapenemase producing organisms/ Enterobacteriacea, Carbapenem resistant organisms Screen on admission patients with recent hospital contact from abroad or high risk UK hospitals. Screen contacts of cases as advised by IPC 3 samples, 48h apart are required. Please ensure that there is visible faecal material on any rectal swabs. MRSA screen 1-3 working days 1-3 working days CSF Cerebrospinal fluid Spinal fluid Investigation of meningitis and other CNS infections. *Bacterial meningitis is a notifiable disease The preferred number of samples is 3 s, which must be numbered consecutively. Sample 2 will be sent to Biochemistry, and any further s will be stored in Microbiology. Please ensure adequate volumes, min 0.5ml (10 drops) per, but ideally 1ml (20 drops). For PCR requests, an additional 1-2 ml (20-40 drops) is preferred, and for AFB investigations >6ml of sample is optimal for adequate sensitivity, but it is understood that this amount of sample will not always be possible. It is safe to remove 15ml of CSF in adults, 4ml in older children and 2ml in children <5 years old. WBC count is less reliable in heavily blood stained samples, and invalid in clotted samples. WBC:RBC ratio of 1:500 to 1:1000 is not indicative of infection. Normal microscopy values are age related: WBC <5 x10^6/l in adults. WBC <30 in neonates. Samples must be delivered immediately by hand (e.g. porter) but must NOT be sent via the vacuum pod system. Please note requests for viral PCRs are not processed automatically if the CSF WC and protein parameters are normal, as infection is unlikely; please discuss the request with the microbiology consultant if PCRs are still required. Microscopy within 2 hours. Culture 3 working days. 1 month CSF viral PCR Cerebrospinal fluid Investigation of meningitis and other CNS infections Sample can be sent to reference labs for additional viral and bacterial PCRs eg. Parechovirus, N. meningitides, S. pneumonia. Please note requests for viral PCRs are not processed automatically if the CSF WC and protein parameters are normal, as infection is unlikely; please discuss the request with the microbiology consultant if PCRs are still required. See above for information on sample volume required. Royal Bournemouth Hospital University of Warwick Science Park, Coventry Meningococcal reference Unit, Manchester RL: 2-3 working days 1 month Page: 4 of 15

5 Diphtheria antibodies Test of functional immunity (IgG) For suspected case of diphtheria see throat swab PHE Manchester, 21 working days (RL: 28 Medical Microbiology Partnership Viral haemorrhagic fever (incl. Ebola virus*) Suspected or possible Ebola/ VHF. Cases MUST be discussed with on call microbiologist first to confirm risk assessment and sampling requirements. See DCH Ebola operational guidance. Rare and Imported Pathogens PHE, Porton Down RL: 1-2 working days EBV serology Epstein-Barr, Glandular fever, Infectious mononucleosis Investigation of glandular fever, PUO, hepatitis IgM, IgG and EBNA are tested. Follow up sample may help determine whether recent infection has occurred. 2 working days 6 months EBV PCR Enterovirus serology EDTA blood Bornholm s disease,. coxsackie virus Detects EBV viraemia in high risk haematology patients. May be suggested by lab to confirm acute infection. Test covers a range of enteroviruses. Test acute and convalescent serum (PCR testing is preferred in acute infection) Bristol Epsom & St.Helier NHS Trust, Surrey 7 working days 7 days 7 working days (RL: 1-8 Enterovirus PCR Throat swab (viral), faeces Bornholm s disease, coxsackie virus Suspected enterovirus infection Test covers a range of enteroviruses Test in acute infection Bristol 7 working days 7 days Eye swab bacterial culture Eye swab MC&S Investigation of bacterial conjunctivitis 3 working days Eye swab virus Eye swab (viral) Adenovirus + Herpes Simplex Investigation of viral conjunctivitis/ keratitis Bristol 5 working days 7 days for culture MC&S For investigation of suspected infective diarrhoea, food poisoning*, enteric fever* /typhoid, Haemolytic uraemic syndrome (HUS)* Please include travel history as additional tests may be indicated 3 working days 7 days for H pylori antigen test False negative results may occur if the patient has been on PP inhibitors, bismuth preparations or antibiotics in the last 2 weeks 1 working day 7 days Norovirus Norovirus PCR, norovirus EIA Testing is performed in outbreak setting on the advice of Infection control, not generally for individual patient management. Will normally be tested by PCR as more sensitive. EIA may be used out of hours but sensitivity only 50% per sample. 1 working days 7 days Parasite microscopy Sensitivity is improved by examining 3 separate samples Please state travel history 3 working days 7 days Page: 5 of 15

6 Fluid/aspirate/pus Fluid Fluid/aspirate/pus Send material if available NOT just a swab 3 working days for solid culture. Additional 4 working days for enrichment culture 1 month Fungal culture Nails, skin scrapings, hair roots Swabs accepted if for yeasts only Tinea, onchomycosis, ringworm, dermatophyte infection For investigation of superficial fungal infections. The best samples are crumbly parts of nail, root end of hair, skin scrapings from edge of lesion. Nails are easily contaminated with environmental fungi. Positive microscopy is more indicative of infection than positive culture alone working days Genital swabs Urethral swab, cervical swab, high vaginal swab, low vaginal swab For investigation of thrush, discharge, bacterial vaginosis. Additional samples (eg chlamydia) required for full STI screen, discuss with GUM. If N. gonorrhoea is suspected, please refer to the GUM, because organism may not survive at low temperature. Please state if pregnant or recent surgery/ instrumentation. 3 working days 7 days H. influenzae antibodies Haemophilus, Hib Test of functional immunity (IgG) PHE Manchester, 20 working days (RL: 28 Medical Microbiology Partnership Filariasis Main species of worms causing filariasis are Loa loa, Wuchereria bancrofti, Onchocerca volvulus, Brugia malayi Investigation of various tropical conditions, usually associated with eosinophila Definitive diagnosis is usually made by peripheral blood film at specific times of day. Please discuss with microbiology consultant. Hospital for Tropical Diseases, London 14 working days Hep A IgM* lithium heparin, EDTA Test in acute hepatitis with raised bilirubin and ALT (usually ALT >400) 1 working day 12 months Hep A IgG lithium heparin, EDTA, citrate Evidence of previous infection or vaccination Bristol 10 working days 2 months Hepatitis B surface antigen lithium heparin HBsAg Test in acute or chronic hepatitis, or to screen people at risk of Hepatitis B infection Marker of circulating virus, chronic or acute infection. May not become positive until up to 3 months after exposure ( window period ) 1 working days. Same day if urgent. 2 months Hep B confirmation markers Hep B e antigen, Hep B e antibody, Hep B core IgM Markers of infectivity, and chronicity of infection. Only performed in positive cases. Positive core IgM indicates recent infection*. Bristol 7 working days Hep B core Ab HBV Viral Load lithium heparin, EDTA, citrate, EDTA To identify patients at risk of reactivation prior to Indicates previous infection immunosuppression, test in conjunction 1 working days 2 months with surface antigen. For infectivity in long term carriers and to monitor treatment Bristol 7 working days 7 days Page: 6 of 15

7 Hep B surface Ab Lithium heparin EDTA (411), citrate (411) For post vaccination testing and needle stick recipients <10 IU/mL = susceptible. >10 IU/mL = Positive responder. Please interpret in conjunction with current guidelines. 1 working day 6 months 3 months (411) Hepatitis C antibody lithium heparin, EDTA (411), citrate (411) Test in suspected chronic hepatitis/ abnormal LFTs, or to screen people at risk of Hepatitis C. HCV antibody may not be detectable early in the infection or at all in immunocompromised patients Positive antibody does not indicate immunity. It indicates cleared or chronic infection. Qualitative PCR distinguishes between these states. 3 working days. Same day if urgent. 12 months (vidas) 3 months (411) HCV genotype EDTA To determine subtype for treatment purposes University of Warwick Science Park, Coventry 7 working days HCV PCR Qualitative PCR To detect chronic/ active infection Confirms infectivity status, and potential for HCV treatment. Bristol 7 working days HCV Viral Load, or EDTA Quantitative PCR May be used to monitor response to treatment 7 working days 7 days Hepatitis D EDTA Delta agent May be indicated in Hepatitis B patients whose liver function deteriorates. Please state if serology or PCR required. Only co-infects with Hepatitis B Virus Reference Division 21 working days (RL: 15 Hep E serology Test in acute hepatitis with raised bilirubin and ALT (usually ALT >400) If immunocompromised, please state on form: lower ALT and chronic infection is possible, PCR may be indicated. 21 working days Herpes simplex virus PCR Herpes simplex serology Swab (viral) of skin lesion / blister fluid EDTA blood CSF see CSF viral PCR, lithium heparin, EDTA HSV 1, HSV 2 HSV type specific serology To confirm suspected herpes rash eg genital herpes, orofacial herpes (swab fluid/ lesions) Investigation of suspected neonatal herpes or disseminated disease in immunocompromised (surface swabs and blood) Occasionally indicated to assess risk of mother to child transmission from genital herpes Can be used to distinguish between primary infection and reactivation May be negative in early infection ( window period ). or Bristol University of Warwick Science Park, Coventry Southampton PHE laboratory 5 working days 7 days 7days 1 month 21 working days 3 working days. Same day if urgent. 2 months 3 months (411) Page: 7 of 15

8 HIV antibody EDTA AIDS Screening test for HIV infection May be negative in early infection ( window period ). First positive results will be confirmed at reference laboratory. Confirmation: Virus Reference Division 14 working days (RL: 8 HIV Viral Load EDTA blood To monitor infectivity and treatment 1 working day HTLV I/II Significant in transplant and milk donors. Blood borne virus. Unusual in UK but common in some countries eg the Caribbean. Not associated with acute illness, usually asymptomatic. Occasional chronic illness (adult T cell lymphoma, tropical spastic Bristol paraparesis). 7 Working days Hydatid Serology Echinococcus granulosus, dog tapeworm Suspected hydatid disease/ cysts Rare in the UK. Associated with sheep and cattle rearing and contact with dogs. Serological cross reactions (false positives) can occur in other parasitic infections, notably larval cestodes and filarial worms and with some neoplasms. False negatives may occur and are common in the case of non-hepatic hydatid cysts Hospital for Tropical Diseases, London 14 Working days Intra Ocular Fluid Procedure Tiny samples produced during procedures Samples from these sites should be inoculated directly onto the surface of agar plates. staff will attend, telephone ext 4343 or call out the duty on-call staff to attend. Ideally they would have 30 minutes notice of the need to attend. This is particularly important out of normal hours where staff will not be on site. 2 working days for solid culture, additional 5 working days for enrichment culture. Influenza PCR Nose/Throat swabs (viral) Bronchial washings/ aspirates Seasonal flu, H1N1 (note that H1N1, previously referred to as swine flu, is now one of the dominant circulating strains of seasonal influenza) Suspected influenza Seasonal flu panel includes circulating Flu A and Flu B. Avian or swine influenza (zoonotic infection) can be tested if requested, at reference lab. Please discuss with consultant microbiologist with animal exposure/ travel details. 1 working day JC virus PML (progressive multifocal leucoencephalopthy) Polyoma virus Serology may be indicated when treating with certain monoclonal antibodies JC virus can cause PML in immunocompromised patients Virus Reference Division 14 Working days (RL: 10 Legionella* urinary Antigen Urine Pontiac fever, legionnaire s disease Rare cause of pneumonia with public health implications. Testing is recommended in severe CAP (CURB65 3). Antigen remain positive for up to days. Antigen does not detect all strains of legionella but does detect those commonly implicated in human disease. Culture is also available if requested on respiratory samples 1 working day Page: 8 of 15

9 Leishmaniasis for serology Tissue for PCR Suspected leishmaniasis Discuss with medical microbiologist, with travel history. A negative result does not exclude visceral leishmaniasis, particularly in HIV positive individuals. Leishmania serology is not helpful in the diagnosis of cutaneous leisnmaniasis. PCR and histology of biopsy material is the best test. Hospital for Tropical Diseases, London 14 Working days Leptospira, or EDTA blood Urine, CSF, Blood culture Weill s disease Suspected leptospirosis Please give possible contact, occupation and leisure activities, and date of symptom onset. Serology usually positive from 5 days after onset of symptoms although antibiotic therapy may delay it. PCR may be performed on acute samples. IgM may be elevated for months or even years with little or no IgG detected Rare and Imported Pathogens PHE, Porton Down 3-7 Working days (RL: 2-4 Lyme Disease, lithium heparin, sodium heparin B. burgdorferi Suspected Lyme disease. Note that erythema migrans should be treated on clinical suspicion. Please include details of symptom onset and tick exposure history. Antibody test may be negative for some weeks (up to 8 weeks) after infection has occurred. Antibody response may be abrogated by antibiotic treatment of early infection. Positive screens are confirmed by reference For confirmation: laboratory Rare and Imported Pathogens PHE, Porton Down 1 working day 6 months Positive requiring confirmation 5-7 working days (RL: 5 Malaria antibody Measles* (IgM) Measles immunity (IgG) EDTA There are very limited indications for this test. Please discuss with microbiology consultant. Investigation of suspected acute malaria is by urgent EDTA blood film examination and antigen (performed by Haematology) In addition to serology, or alternatively, ALL cases of suspected measles should be tested by oral fluid using salivary test kit, available from HPU Tel: 0300 Suspected measles Please discuss with microbiology if urgent result is required for management of patient or contacts May be indicated in pregnant or immunocompromised patients exposed to measles Test may not detect low levels of circulating antibody. Discuss with consultant microbiologist if post exposure prophylaxis of a vulnerable measles contact is being considered. London School of Hygiene & Tropical Medicine, London Virus Reference Division 14 working days 4 working for serology (RL: 4 1 working day info not provided Bristol 1 Working days Page: 9 of 15

10 Measles PCR Bristol 7 days Meningococcal* PCR EDTA blood, CSF, pleural fluid Neisseria meningitidis Investigation of suspected meningococcal disease, especially if blood and /or CSF cultures are negative S. pneumonia on CSF may be included if specified Heparinised, clotted blood, serum or citrated samples can be tested, but EDTA is preferred. Whole CSF (i.e. an uncentrifuged specimen) should PHE Manchester, 2-3 working days (RL:3 be sent in small sterile containers such as a sterile Medical Microbiology 2mL screw capped vial (rather than universal Partnership containers). Where a CSF sample is available, this should be sent in addition to an EDTA blood sample 7 days Mumps* IgM IgG Mycoplasma PCR Orf Parvovirus IgM Parvovirus IgG EDTA Throat swab (viral), CSF Biopsy specimens are preferable for suspected orf. Suitable alternative specimens are either smears of vesicle fluid dried onto a microscope slide, or a piece of crust or biopsy of the lesion placed in a dry container. Parapox virus, contagious pustular dermatosis Parvovirus infection. Slapped cheek. Parvovirus - immunity 16S PCR Tissue, fluids Broad range PCR Suspected mumps Suspected mycoplasma infection. Please discuss with consultant microbiologist. Test available for pregnant women, for investigation of rash illness. Booking bloods can be tested retrospectively to compare with current blood Test available for pregnant women pregnancy, if contact with a rash illness occurs. Booking bloods can be tested retrospectively. May be helpful where infection is suspected but deep specimen eg joint fluid is culture negative. Discuss with microbiology consultant to arrange. In addition to serology, or alternatively, suspected mumps can be tested by oral fluid using salivary test kit, available from HPU Tel: Please discuss with microbiology if urgent result is required for management of patient. Acquired by contact with infected sheep or goats. Please give exposure details. Please note swabs of skin lesions in liquid media are not recommended for electron microscopy Positive IgG at the point of contact with a rash illness indicates immunity. Negative IgG indicates patient is susceptible to parvovirus. Susceptible pregnant contacts should have follow up testing at 4 weeks Detects DNA from any bacterial species, but is less sensitive than organism-specific PCR tests. Bristol Virus Reference Division University of Warwick Science Park, Coventry Virus Reference Division Bristol Great Ormond Street Hospital 5 Working days RL: 10 days) 7 working days 4 working days 5 working days 5 working days 5 working days Up to 1 month Page: 10 of 15

11 PCP PNEUMOCYSTIS JIROVECII Pneumococcal Antibodies Pneumococcal urinary Antigen EDTA blood, BAL, Sputum Urine Test of functional immunity (IgG) Testing is recommended in severe community acquired pneumonia (CURB65 3).). A negative result does not exclude pneumococcal infection. PHE Manchester, Medical Microbiology 4 working days EDTA 7 days BAL 1 month Partnership PHE Manchester, Medical Microbiology 20 working days Partnership 1 working day Rabies Serum Vet lab agency 20 working days PCR panel includes Full respiratory PCR panel usually influenza A&B, reserved for immunosuppressed Nose/Throat swab (viral) adenovirus, RSV, Respiratory virus PCR patients. 5 working days 7 days Bronchial washings parainfluenza, human Influenza A&B testing is available on Bristol metapneumovirus, site see influenza PCR. rhinovirus. Respiratory serology Atypical respiratory pathogen CFTs. Panel may include Q fever (Coxiella burnetii), legionella, Mycoplasma, Chlamydia pneumoniae, Chlamydia psittici, influenza A & B, RSV, adenovirus. Investigation of atypical pneumonia Detects antibody response to infection. May be negative early in illness. A convalescent sample should be tested too. Please give full clinical details including date of onset, Bristol exposure history, travel etc to ensure relevant tests are performed 10 working days Rickettsia Rotavirus RSV test pack Rubella IgG Rubella IgM*, EDTA blood Eschar biopsy / CSF / swab NPA in transport medium lithium heparin, EDTA Different rickettsial species cause travelrelated, insect borne infections including Typhus, Rocky mountain spotted fever. Combined Adenovirus/ rotavirus EIA German Measles - immunity German Measles - infection Investigation of diarrhoea in children Investigation of bronchiolitis Screening of health care workers or pregnant women having contact with a rash illness. It is essential to include contact date and details. Test if current infection is suspected, or for investigation of rash illness in pregnancy. Please give onset date and any contact dates. Requestor should discuss with microbiology consultant as cases are likely to need discussion with Rare and Imported PHE Imported Fever Service. Pathogens It is essential to state countries visited, duration of stay and return date with full clinical details and PHE, Porton Down vaccines given Positive results in neonates must be confirmed by ref lab, which may lengthen turnaround time in this age group. RSV rapid testing is not as sensitive as PCR. A negative result does not exclude RSV infection. As of April 2016, this is no longer included in routine antenatal bloods, as per PHE guidance. History of vaccination should be documented instead. 3-7 working days (RL: working day 7 days 1 working day 1 working day. 2 months Bristol 5 working days Page: 11 of 15

12 Shistosomiasis serology Schistosomiasis microscopy Terminal urine (S. haematobium ) (S. mansoni, S japonicum) Bilharzia, S haematobium, S mansoni, S japonicum Schistosomes, ova Test if acute or chronic schistosomiasis is suspected. Asymptomatic individuals with exposure to fresh water in endemic areas should be tested 12 weeks after exposure. Antibody takes 6-12 weeks to develop. Check dipstick for haematuria and FBC for eosinophilia. Serology does not distinguish between active or treated infections, nor the species. Diagnosis should be confirmed by detection of ova in urine or stool where possible, as false positive serology can occur (send 3x stool and a terminal urine) Test if acute or chronic schistosomiasis Eggs may not appear in urine/stool until some is suspected. months after infection Test in patients with positive serology. Hospital for Tropical Diseases, London 14 Working days 3 working days 7 days Sputum for culture Sputum and Bronchoalveolar lavages Investigation of lower respiratory tract infection and pneumonia Please indicate if sputum is from a patient with cystic fibrosis, or if TB or fungal infection is suspected, as additional culture will be performed. 3 working days BALs 4 weeks. Sputums require fresh sample. Page: 12 of 15

13 Syphilis serology lithium heparin, EDTA, citrate Lues, Wasserman,WR,VDRL, RPR,TPHA Antenatal and STI screening, or in suspected syphilis or congenital infection. Primary screening test performed in house. Positive samples will be sent to reference for confirmation and further markers eg RPR. Antibodies may not become positive for 6-12 weeks for confirmation: from exposure ( window period ), and may be negative for up to 2 weeks after development of chancre. Bristol 3 working days. Same day if urgent. 12 months Trypanosomiasis TB microscopy and culture* Sputum, urine, Bronchoalveloar lavages, tissues, CSFs African trypanosiasis (T brucei ) - Sleeping sickness. American trypanosomiasis (T. cruzi ) Chagas diseases. Mycobacterial culture Discuss with medical microbiologist. Examination of fresh blood films may be indicated. Positive cultures will be sent to reference laboratory for speciation and sensitivity testing Suspected TB. Culture detects M. TB PCR is available for a rapid result when clinically rculosis and atypical mycobacteria. indicated, please discuss with consultant microbiologist Hospital for Tropical Diseases, London Positives and rapid PCR sent to Public Health National Mycobacterium Reference Unit, 14 Working days Microscopy 24hrs. Culture 1-6 weeks TB PCR 72h Tissues, BALs and CSFs 4 weeks. Sputums that have already been cultured for routine organisms cannot be subsequently investigated for TB. Routine urine samples are not suitable for TB investigations. Tetanus Ab Response to tetanus vaccine may be used to assess immunodeficiency. In suspected tetanus*, collect a baseline sample before tetanus immunoglobulin is administered. Please include indication for test. Discuss any case of suspected tetanus with microbiology consultant PHE Manchester, 20 working days (RL: 28 Medical Microbiology Partnership Thread worms microscopy Sellotape slide pin worms Suspected threadworms. Investigation of pruritis ani in children Sellotape slide - impression of anal area taken with clear tape and stick to one side of glass slide. 3 working days Throat swab for bacterial culture Swab MC&S Please include any travel history or if diphtheria is suspected. Please specify if part of meningitis screen (detection of N. meningitidis) 3 working days Tissue Tissue MC&S If sample is small and at risk of drying out, add a little sterile saline. 2 working days for solid culture, additional 6 working days for enrichment culture. Toxocara Dog round worm, T canis Investigation of ocular or visceral larva migrans. Negative serum result does not exclude ocular toxocara; vitreous sampling may be required. Hospital for Tropical Diseases, London 14 Working days Page: 13 of 15

14 Toxoplasma lithium heparin, EDTA Positive screens are sent to reference laboratory for confirmation 1 working day 2 months Swansea Public Health, Swansea 14 working days T-spot TB test Whole blood TB interferon gamma release assay (IGRA) TB Elispot Used to detect latent TB by showing a cell-mediated immune response to TB antigens. Only accepted following discussion with Consultant Microbiologist, or respiratory physician. Cannot distinguish between latent or active TB. Not affected by prior BCG vaccination. Do not send samples through vacuum system. MUST BE FRESHLY COLLECTED AND DELIVERED BY HAND mon-thurs only, before 3.30pm, and by prior agreement. Do not refrigerate Oxford Diagnostic Laboratories 3 working days Fresh sample always required. Urine microscopy and culture Urine MC&S Diagnosis of urinary tract infection. To reduce contamination, samples should ideally be a clean catch, mid stream specimen. Please include clinical details and antibiotic therapy. CSUs from long term catheters should only be sent when there are clinical signs of UTI or sepsis. 1 working day VZV immunity Chicken pox, varicella zoster virus For assessment of immunity, usually in pregnant or immunocompromised patients For pregnant or immunocompromised patients who have had contact with chicken pox or shingles, it is essential to give contact date. testing is not required in pregnant women who have a history of chicken pox in the past. Negative or equivocal IgG results need to be confirmed by reference lab. Please discuss if VZIG may be required urgently (ie approaching 7-10 days since contact with chicken pox) 1 working day for confirmation: Bristol 2 working days VZV PCR Vesicle fluid skin swab varicella zoster virus Can be used to confirm acute chicken pox or shingles, eg if atypical features Bristol 3 working days VZIgM Chicken pox, varicella zoster virus To demonstrate recent infection. Not useful for Shingles Epsom & St.Helier NHS Trust, Surrey 7 working days (RL: 1-5 Page: 14 of 15

15 Wound swab for bacterial culture Swab MC&S Investigation of skin and soft tissue infection Surface swabs cannot differentiate infection from colonisation. Please send only if clinical signs of infection. If pus is available, please send this in a sterile container rather than a swab. Include full clinical history, and whether related to surgery 3 working days 7 days Yersinia Tissue Yersinia serology is currently not available, culture of stool or tissue is available, if requested specifically. 3 working days 7 days Zika virus +/- EDTA blood Urine Suspected zika infection in pregnant woman. Must be discussed with microbiology consultant, including symptom onset and travel history Rare and Imported Pathogens PHE, Porton Down 5-7 working days Page: 15 of 15